List of usage examples for com.mongodb BasicDBObject getInt
public int getInt(final String key)
From source file:org.mybatis.jpetstore.domain.Order.java
License:Apache License
public static Order fromDBObject(@Nonnull final DBObject dbObj) { checkNotNull(dbObj, "Argument[dbObj] must not be null"); BasicDBObject orderObj = (BasicDBObject) dbObj; Order order = new Order(); order.setOrderId(orderObj.getInt("order_id")); order.setUsername(orderObj.getString("username")); order.setOrderDate(orderObj.getDate("order_date")); order.setCourier(orderObj.getString("courier")); String totalPrice = orderObj.getString("total_price"); if (!isNullOrEmpty(totalPrice)) { order.setTotalPrice(new BigDecimal(totalPrice)); }/* w ww . j a va 2s . c o m*/ order.setLocale(orderObj.getString("locale")); order.setStatus(orderObj.getString("status")); BasicDBObject shipToObj = (BasicDBObject) orderObj.get("shipping_address"); order.setShipToFirstName(shipToObj.getString("ship_to_firstname")); order.setShipToLastName(shipToObj.getString("ship_to_lastname")); order.setShipAddress1(shipToObj.getString("ship_address_1")); order.setShipAddress2(shipToObj.getString("ship_address_2")); order.setShipCity(shipToObj.getString("ship_city")); order.setShipState(shipToObj.getString("ship_state")); order.setShipZip(shipToObj.getString("ship_zip")); order.setShipCountry(shipToObj.getString("ship_country")); BasicDBObject billToObj = (BasicDBObject) orderObj.get("billing_address"); order.setBillToFirstName(billToObj.getString("bill_to_firstname")); order.setBillToLastName(billToObj.getString("bill_to_lastname")); order.setBillAddress1(billToObj.getString("bill_address_1")); order.setBillAddress2(billToObj.getString("bill_address_2")); order.setBillCity(billToObj.getString("bill_city")); order.setBillState(billToObj.getString("bill_state")); order.setBillZip(billToObj.getString("bill_zip")); order.setBillCountry(billToObj.getString("bill_country")); BasicDBObject paymentInfoObj = (BasicDBObject) orderObj.get("payment_info"); order.setCreditCard(paymentInfoObj.getString("credit_card")); order.setExpiryDate(paymentInfoObj.getString("expiry_date")); order.setCardType(paymentInfoObj.getString("card_type")); List<DBObject> lineItemObjs = (ArrayList<DBObject>) orderObj.get("line_items"); List<LineItem> lineItems = new ArrayList<>(); for (DBObject lineItemObj : lineItemObjs) { LineItem lineItem = LineItem.fromDBObject(lineItemObj); lineItem.setOrderId(order.getOrderId()); lineItems.add(lineItem); } order.setLineItems(lineItems); return order; }
From source file:org.mybatis.jpetstore.domain.Sequence.java
License:Apache License
public static Sequence fromDBObject(@Nullable final BasicDBObject sequenceObj) { Sequence sequence = null;/* w w w . j av a2 s.c o m*/ if (sequenceObj != null) { String name = sequenceObj.getString("name"); Integer nextId = sequenceObj.getInt("next_id"); sequence = new Sequence(name, nextId); } return sequence; }
From source file:org.opencb.cellbase.mongodb.db.ConservationMongoDBAdaptor.java
License:Apache License
@Deprecated @Override/*w w w .ja v a 2s. c o m*/ public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) { //TODO not finished yet List<DBObject> queries = new ArrayList<>(); List<String> ids = new ArrayList<>(regions.size()); List<String> integerChunkIds; for (Region region : regions) { integerChunkIds = new ArrayList<>(); // positions below 1 are not allowed if (region.getStart() < 1) { region.setStart(1); } if (region.getEnd() < 1) { region.setEnd(1); } /****/ QueryBuilder builder; int regionChunkStart = getChunkId(region.getStart(), this.chunkSize); int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize); if (regionChunkStart == regionChunkEnd) { builder = QueryBuilder.start("_chunkIds") .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), this.chunkSize)); } else { // for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) { //// integerChunkIds.add(chunkId); // integerChunkIds.add(region.getChromosome() + "_" + chunkId + "_" + this.chunkSize/1000 + "k"); // } // builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds); builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end") .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd()); } // QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(hunkIds); /****/ queries.add(builder.get()); ids.add(region.toString()); logger.info(builder.get().toString()); } List<QueryResult> queryResults = executeQueryList(ids, queries, options); for (int i = 0; i < regions.size(); i++) { Region region = regions.get(i); QueryResult queryResult = queryResults.get(i); BasicDBList list = (BasicDBList) queryResult.getResult(); Map<String, List<Float>> typeMap = new HashMap(); // int start = region.getStart(); for (int j = 0; j < list.size(); j++) { BasicDBObject chunk = (BasicDBObject) list.get(j); String type = chunk.getString("type"); List<Float> valuesList; if (!typeMap.containsKey(type)) { valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1); for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) { valuesList.add(null); } typeMap.put(type, valuesList); } else { valuesList = typeMap.get(type); } BasicDBList valuesChunk = (BasicDBList) chunk.get("values"); int pos = 0; if (region.getStart() > chunk.getInt("start")) { pos = region.getStart() - chunk.getInt("start"); } for (; pos < valuesChunk.size() && (pos + chunk.getInt("start") <= region.getEnd()); pos++) { // System.out.println("valuesList SIZE = " + valuesList.size()); // System.out.println("pos = " + pos); // System.out.println("DIV " + (chunk.getInt("start") - region.getStart())); // System.out.println("valuesChunk = " + valuesChunk.get(pos)); // System.out.println("indexFinal = " + (pos + chunk.getInt("start") - region.getStart())); valuesList.set(pos + chunk.getInt("start") - region.getStart(), new Float((Double) valuesChunk.get(pos))); } } // BasicDBList resultList = new BasicDBList(); ConservedRegionFeature conservedRegionChunk; for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) { conservedRegionChunk = new ConservedRegionFeature(region.getChromosome(), region.getStart(), region.getEnd(), elem.getKey(), elem.getValue()); resultList.add(conservedRegionChunk); } queryResult.setResult(resultList); } return queryResults; }
From source file:org.opencb.cellbase.mongodb.db.ConservationMongoDBAdaptor.java
License:Apache License
@Override public List<QueryResult> getAllScoresByRegionList(List<Region> regions, QueryOptions options) { //TODO not finished yet List<DBObject> queries = new ArrayList<>(); List<String> ids = new ArrayList<>(regions.size()); List<Integer> integerChunkIds; for (Region region : regions) { integerChunkIds = new ArrayList<>(); // positions below 1 are not allowed if (region.getStart() < 1) { region.setStart(1);//from w w w .ja v a 2 s .c o m } if (region.getEnd() < 1) { region.setEnd(1); } /****/ QueryBuilder builder; int regionChunkStart = getChunkId(region.getStart(), this.chunkSize); int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize); if (regionChunkStart == regionChunkEnd) { builder = QueryBuilder.start("_chunkIds") .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), chunkSize)); } else { // for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) { // integerChunkIds.add(chunkId); // } // // QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(hunkIds); // builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds); builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end") .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd()); } /****/ queries.add(builder.get()); ids.add(region.toString()); logger.info(builder.get().toString()); } List<QueryResult> queryResults = executeQueryList2(ids, queries, options); // List<QueryResult> queryResults = executeQueryList(ids, queries, options); for (int i = 0; i < regions.size(); i++) { Region region = regions.get(i); QueryResult queryResult = queryResults.get(i); List<BasicDBObject> list = (List<BasicDBObject>) queryResult.getResult(); Map<String, List<Float>> typeMap = new HashMap(); // int start = region.getStart(); for (int j = 0; j < list.size(); j++) { BasicDBObject chunk = (BasicDBObject) list.get(j); String type = chunk.getString("type"); List<Float> valuesList; if (!typeMap.containsKey(type)) { valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1); for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) { valuesList.add(null); } typeMap.put(type, valuesList); } else { valuesList = typeMap.get(type); } BasicDBList valuesChunk = (BasicDBList) chunk.get("values"); int pos = 0; if (region.getStart() > chunk.getInt("start")) { pos = region.getStart() - chunk.getInt("start"); } for (; pos < valuesChunk.size() && (pos + chunk.getInt("start") <= region.getEnd()); pos++) { valuesList.set(pos + chunk.getInt("start") - region.getStart(), new Float((Double) valuesChunk.get(pos))); } } BasicDBList resultList = new BasicDBList(); for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) { for (Float value : elem.getValue()) { resultList.add(value != null ? (new Score(new Double(value), elem.getKey())) : null); } } queryResult.setResult(resultList); } return queryResults; }
From source file:org.opencb.cellbase.mongodb.db.core.ConservationMongoDBAdaptor.java
License:Apache License
@Deprecated @Override//from ww w.j a va 2s .co m public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) { //TODO not finished yet List<DBObject> queries = new ArrayList<>(); List<String> ids = new ArrayList<>(regions.size()); List<String> integerChunkIds; for (Region region : regions) { integerChunkIds = new ArrayList<>(); // positions below 1 are not allowed if (region.getStart() < 1) { region.setStart(1); } if (region.getEnd() < 1) { region.setEnd(1); } // Max region size is 10000bp if (region.getEnd() - region.getStart() > 10000) { region.setEnd(region.getStart() + 10000); } QueryBuilder builder; int regionChunkStart = getChunkId(region.getStart(), this.chunkSize); int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize); if (regionChunkStart == regionChunkEnd) { builder = QueryBuilder.start("_chunkIds") .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), this.chunkSize)); } else { // for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) { //// integerChunkIds.add(chunkId); // integerChunkIds.add(region.getChromosome() + "_" + chunkId + "_" + this.chunkSize/1000 + "k"); // } // builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds); builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end") .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd()); } // QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(hunkIds); /****/ queries.add(builder.get()); ids.add(region.toString()); logger.debug(builder.get().toString()); } List<QueryResult> queryResults = executeQueryList2(ids, queries, options); for (int i = 0; i < regions.size(); i++) { Region region = regions.get(i); QueryResult queryResult = queryResults.get(i); // BasicDBList list = (BasicDBList) queryResult.getResult(); List list = queryResult.getResult(); Map<String, List<Float>> typeMap = new HashMap(); // int start = region.getStart(); for (int j = 0; j < list.size(); j++) { BasicDBObject chunk = (BasicDBObject) list.get(j); String type = chunk.getString("type"); List<Float> valuesList; if (!typeMap.containsKey(type)) { valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1); for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) { valuesList.add(null); } typeMap.put(type, valuesList); } else { valuesList = typeMap.get(type); } BasicDBList valuesChunk = (BasicDBList) chunk.get("values"); int pos = 0; if (region.getStart() > chunk.getInt("start")) { pos = region.getStart() - chunk.getInt("start"); } for (; pos < valuesChunk.size() && (pos + chunk.getInt("start") <= region.getEnd()); pos++) { // System.out.println("valuesList SIZE = " + valuesList.size()); // System.out.println("pos = " + pos); // System.out.println("DIV " + (chunk.getInt("start") - region.getStart())); // System.out.println("valuesChunk = " + valuesChunk.get(pos)); // System.out.println("indexFinal = " + (pos + chunk.getInt("start") - region.getStart())); valuesList.set(pos + chunk.getInt("start") - region.getStart(), new Float((Double) valuesChunk.get(pos))); } } // BasicDBList resultList = new BasicDBList(); ConservedRegionFeature conservedRegionChunk; for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) { conservedRegionChunk = new ConservedRegionFeature(region.getChromosome(), region.getStart(), region.getEnd(), elem.getKey(), elem.getValue()); resultList.add(conservedRegionChunk); } queryResult.setResult(resultList); } return queryResults; }
From source file:org.opencb.cellbase.mongodb.db.core.ConservationMongoDBAdaptor.java
License:Apache License
@Override public List<QueryResult> getAllScoresByRegionList(List<Region> regions, QueryOptions options) { //TODO not finished yet List<DBObject> queries = new ArrayList<>(); List<String> ids = new ArrayList<>(regions.size()); List<Integer> integerChunkIds; for (Region region : regions) { integerChunkIds = new ArrayList<>(); // positions below 1 are not allowed if (region.getStart() < 1) { region.setStart(1);/*from w w w .j ava 2 s . co m*/ } if (region.getEnd() < 1) { region.setEnd(1); } /****/ QueryBuilder builder; int regionChunkStart = getChunkId(region.getStart(), this.chunkSize); int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize); if (regionChunkStart == regionChunkEnd) { builder = QueryBuilder.start("_chunkIds") .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), chunkSize)); } else { // for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) { // integerChunkIds.add(chunkId); // } // // QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(hunkIds); // builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds); builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end") .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd()); } /****/ queries.add(builder.get()); ids.add(region.toString()); logger.debug(builder.get().toString()); } List<QueryResult> queryResults = executeQueryList2(ids, queries, options); // List<QueryResult> queryResults = executeQueryList(ids, queries, options); for (int i = 0; i < regions.size(); i++) { Region region = regions.get(i); QueryResult queryResult = queryResults.get(i); List<BasicDBObject> list = (List<BasicDBObject>) queryResult.getResult(); Map<String, List<Float>> typeMap = new HashMap(); // int start = region.getStart(); for (int j = 0; j < list.size(); j++) { BasicDBObject chunk = (BasicDBObject) list.get(j); String type = chunk.getString("type"); List<Float> valuesList; if (!typeMap.containsKey(type)) { valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1); for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) { valuesList.add(null); } typeMap.put(type, valuesList); } else { valuesList = typeMap.get(type); } BasicDBList valuesChunk = (BasicDBList) chunk.get("values"); int pos = 0; if (region.getStart() > chunk.getInt("start")) { pos = region.getStart() - chunk.getInt("start"); } for (; pos < valuesChunk.size() && (pos + chunk.getInt("start") <= region.getEnd()); pos++) { valuesList.set(pos + chunk.getInt("start") - region.getStart(), new Float((Double) valuesChunk.get(pos))); } } BasicDBList resultList = new BasicDBList(); for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) { for (Float value : elem.getValue()) { if (value != null) { resultList.add(new Score(new Double(value), elem.getKey())); } } } if (!resultList.isEmpty()) { queryResult.setResult(resultList); } else { queryResult.setResult(null); } } return queryResults; }
From source file:org.opencb.cellbase.server.ws.feature.GeneWSServer.java
License:Apache License
@GET @Path("/{geneId}/snp") @ApiOperation(httpMethod = "GET", value = "Get all SNPs within the specified gene(s)") public Response getSNPByGeneId(@PathParam("geneId") String query) { try {//from w w w . ja v a 2 s .co m parseQueryParams(); GeneDBAdaptor geneDBAdaptor = dbAdaptorFactory.getGeneDBAdaptor(this.species, this.assembly); VariationDBAdaptor variationDBAdaptor = dbAdaptorFactory.getVariationDBAdaptor(this.species, this.assembly); List<QueryResult> qrList; if (queryOptions.containsKey("count") && queryOptions.getBoolean("count")) { queryOptions.remove("count"); qrList = geneDBAdaptor.getAllByIdList(Splitter.on(",").splitToList(query), queryOptions); queryOptions.put("count", true); } else { qrList = geneDBAdaptor.getAllByIdList(Splitter.on(",").splitToList(query), queryOptions); } List<QueryResult> queryResults = new ArrayList<>(); for (QueryResult qr : qrList) { QueryResult queryResult = new QueryResult(); queryResult.setId(qr.getId()); // FIXME MongoDB code should not be here BasicDBObject gene = (BasicDBObject) qr.getResult().get(0); QueryResult variationQueryResult = variationDBAdaptor.getAllByRegion(gene.getString("chromosome"), gene.getInt("start"), gene.getInt("end"), queryOptions); queryResult.setNumResults(variationQueryResult.getNumResults()); queryResult.setResult(variationQueryResult.getResult()); queryResults.add(queryResult); } return createOkResponse(queryResults); } catch (Exception e) { return createErrorResponse(e); } }
From source file:org.opendaylight.controller.samples.onftappingapp.RewriteParams.java
License:Apache License
public RewriteParams(BasicDBObject objDoc) throws UnknownHostException { this.setName(objDoc.getString("name")); this.setIPAddress((String) objDoc.get("IPAddress")); this.setMacAddr((String) objDoc.getString("MACAddress")); this.setVlanId((int) objDoc.getInt("VLAN_ID")); }
From source file:org.openhab.persistence.mongodb.internal.MongoDBPersistenceService.java
License:Open Source License
@Override public Iterable<HistoricItem> query(FilterCriteria filter) { if (!initialized) { return Collections.emptyList(); }/* w ww.ja v a2 s . c o m*/ if (!isConnected()) { connectToDatabase(); } if (!isConnected()) { return Collections.emptyList(); } String name = filter.getItemName(); Item item = getItem(name); List<HistoricItem> items = new ArrayList<HistoricItem>(); DBObject query = new BasicDBObject(); if (filter.getItemName() != null) { query.put(FIELD_ITEM, filter.getItemName()); } if (filter.getState() != null && filter.getOperator() != null) { String op = convertOperator(filter.getOperator()); Object value = convertValue(filter.getState()); query.put(FIELD_VALUE, new BasicDBObject(op, value)); } if (filter.getBeginDate() != null) { query.put(FIELD_TIMESTAMP, new BasicDBObject("$gte", filter.getBeginDate())); } if (filter.getEndDate() != null) { query.put(FIELD_TIMESTAMP, new BasicDBObject("$lte", filter.getEndDate())); } Integer sortDir = (filter.getOrdering() == Ordering.ASCENDING) ? 1 : -1; DBCursor cursor = this.mongoCollection.find(query).sort(new BasicDBObject(FIELD_TIMESTAMP, sortDir)) .skip(filter.getPageNumber() * filter.getPageSize()).limit(filter.getPageSize()); while (cursor.hasNext()) { BasicDBObject obj = (BasicDBObject) cursor.next(); final State state; if (item instanceof NumberItem) { state = new DecimalType(obj.getDouble(FIELD_VALUE)); } else if (item instanceof DimmerItem) { state = new PercentType(obj.getInt(FIELD_VALUE)); } else if (item instanceof SwitchItem) { state = OnOffType.valueOf(obj.getString(FIELD_VALUE)); } else if (item instanceof ContactItem) { state = OpenClosedType.valueOf(obj.getString(FIELD_VALUE)); } else if (item instanceof RollershutterItem) { state = new PercentType(obj.getInt(FIELD_VALUE)); } else if (item instanceof ColorItem) { state = new HSBType(obj.getString(FIELD_VALUE)); } else if (item instanceof DateTimeItem) { Calendar cal = Calendar.getInstance(); cal.setTime(obj.getDate(FIELD_VALUE)); state = new DateTimeType(cal); } else { state = new StringType(obj.getString(FIELD_VALUE)); } items.add(new MongoDBItem(name, state, obj.getDate(FIELD_TIMESTAMP))); } return items; }
From source file:org.sdsai.dsds.mongo.MongoUtils.java
License:Open Source License
public static Object getPrimitive(final BasicDBObject dbo, final String fieldName, final Class<?> returnType) throws Exception { final boolean contained = dbo.containsField(fieldName); if (Boolean.TYPE.equals(returnType)) return contained ? dbo.getBoolean(fieldName) : Boolean.FALSE; if (Short.TYPE.equals(returnType) || Byte.TYPE.equals(returnType) || Integer.TYPE.equals(returnType)) return (Integer) (contained ? dbo.getInt(fieldName) : 0); if (Character.TYPE.equals(returnType)) return (Character) ((dbo.get(fieldName) + "").charAt(0)); if (Long.TYPE.equals(returnType)) return (Long) (contained ? dbo.getLong(fieldName) : 0L); if (Float.TYPE.equals(returnType)) return (Float) (contained ? Float.valueOf(dbo.get(fieldName) + "") : 0F); if (Double.TYPE.equals(returnType)) return (Double) (contained ? dbo.getDouble(fieldName) : 0D); return null;/*from ww w.j av a 2 s . com*/ }